BN1822 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.4020e-07 2.5121e-03
Layer 2 6.5217e-07 3.6576e-04
Layer 4 9.3219e-07 7.3749e-05
Layer 6 1.0906e-04 1.3753e-02
Layer 5 1.1274e-04 1.0081e-03
Layer 1 5.6711e-02 1.5092e-01
WM 9.9610e-01 5.6783e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
RTN1 Expression Distribution
Gene Specificity Score (GSS)
RTN1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
RTN1 Layer 4 3.1875 0.8074
SARAF Layer 4 3.1465 0.8046
NAPB Layer 4 3.2793 0.8028
TSPAN7 Layer 4 3.4902 0.8007
NDRG4 Layer 4 3.4824 0.8005
ATP1B1 Layer 4 3.1797 0.7993
STXBP1 Layer 4 3.5508 0.7982
MORF4L1 Layer 4 3.1875 0.7978
BEX3 Layer 5 2.9805 0.7975
ENO2 Layer 4 3.2715 0.7975
SLC22A17 Layer 4 3.3281 0.7963
NGRN Layer 4 3.3281 0.7949
KLC1 Layer 4 3.1387 0.7945
STMN3 Layer 4 3.4375 0.7940
PNMA2 Layer 4 3.7148 0.7939
YWHAH Layer 4 2.9805 0.7938
SNRPN Layer 4 3.4375 0.7935
BEX1 Layer 2 3.3223 0.7931
FAIM2 Layer 4 3.4160 0.7929
NDFIP1 Layer 4 3.0391 0.7924
EIF4A2 Layer 4 3.3652 0.7912
WBP2 Layer 4 3.0918 0.7910
SERINC1 Layer 4 2.9863 0.7903
ARF1 Layer 2 3.1523 0.7901
ATP2B2 Layer 4 3.2930 0.7891
RTN3 Layer 4 3.1191 0.7890
ATP5F1A Layer 4 3.0781 0.7888
PREPL Layer 4 3.4004 0.7885
UQCRH Layer 4 3.5820 0.7885
CFL1 Layer 4 3.0195 0.7884
EEF1A2 Layer 4 3.3867 0.7877
RNF11 Layer 4 2.9473 0.7877
MEF2C Layer 4 3.3438 0.7877
YWHAG Layer 4 3.1660 0.7871
ARL6IP1 Layer 4 3.1934 0.7868
NEFL Layer 4 3.3867 0.7868
TSC22D1 Layer 4 3.0527 0.7867
PLD3 Layer 2 3.0449 0.7865
CLIP3 Layer 4 3.0312 0.7865
AP2M1 Layer 4 3.4902 0.7862
ATP1A1 Layer 4 3.3145 0.7856
SPTAN1 Layer 4 3.2090 0.7854
TBCB Layer 4 2.4727 0.7852
RAB6B Layer 5 3.2930 0.7851
GDI1 Layer 4 3.0645 0.7848
FXYD6 Layer 4 3.3223 0.7844
CABP1 Layer 4 3.1875 0.7841
SYN1 Layer 4 3.2578 0.7840
OAZ1 Layer 4 3.0996 0.7838
CTSB Layer 4 2.7656 0.7836

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1822
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1822_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1822/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1822/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1822/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1822/report/PD/BN1822_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1822/report/PD/BN1822_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:57:37
  • Number of Processes: 10
  • Spending Time: 0h 4m